Periodic Reporting for period 2 - BIG4 (BIG4 - Biosystematics, Informatics and Genetics of the big 4 insect groups: training tomorrow's researchers and entrepreneurs)
Reporting period: 2017-01-01 to 2018-12-31
BIG4 aimed to train a new generation of researchers to explore the biggest chunk of Earth biodiversity, the four mega-diverse insect orders: beetles; bees, wasps, ants; flies and mosquitoes; as well as butterflies and moths. It combined the cutting edge methods of genomics, phylogenetics, informatics, taxonomy, semantic biodiversity publishing and citizen science and ran a cross-disciplinary training programme for 16 Early Stage Researchers (ESRs) with a stronghold in biosystematics. One ESRs secured a competitive permanent position as researcher and collections curator at the Canadian National Collection of Insects and Arthropods and was replaced by an ESR who is two years into her training. Another ESR took up a programing and data visualisation job in the industry. Three ESRs successfully defended their PhD theses in 2019, and one already secured a post doctoral position to continue to research on rove beetle systematics. The other two, after their PhD defences, are poised to get post doctoral scholarships or a job, most likely in academia. Three more ESRs have completed their PhD with defence scheduled in 2019. The remaining ESRs are on a four year PhD program and well on track with their projects. Thanks to the collaborative spirit and synergistic environment of the BIG4 action, all ESRs are on the track to explore the four biggest groups of living organisms in ways never tried before. The main objective of BIG4, meeting the urgent need to focus on the “big four” insect groups by training young generation researchers and entrepreneurs, is fulfilled. As future leaders in the field the ESRs will continue to exploit the huge potential of that biological diversity. BIG4 succeeded in integrating academia with business (genomic, big data visualisation and automated insect identification projects) and the public (citizen-science). BIG4 made the insect mega-diversity much more visible as a powerful service for economic and societal needs such as environmental monitoring, biological control, biomedicine, or ecological farming.
BIG4 recruited all ESRs, created a BIG4 website serving as communication platform which will continue to be updated with news on upcoming papers, PhDs and other BIG4 impact and held all planned training workshops/summer schools, sometimes tied to workshops on e.g. museum collections management or grant-writing, job search, advanced science publishing etc. BIG4 ensured smooth progress of all ESRs’ projects, published many peer review papers also in high impact journals, delivered posters and presentations at international and local scientific conferences or other events. It provided outreach activities (articles, social media posts, newspaper publications, interviews) and ensured all PhD theses meet the highest standards. Overall, BIG4 created a very effective and friendly training and research environment, stimulating collaboration among students and supervisors.
All BIG4 activities are at the crossroads of several Workpackages: WP1, Big data sets assembly and compatibility for biosystematics, begun data collection. WP1 trained ESRs in extraction of huge DNA data from the suboptimal museum insect specimens, with first samples of Lepidoptera. Some ESRs produced big genomic or morphological data for a taxon-based and bulk sample-based project, which meant learning programming and de novo genome assembly for large-scale phylogenetic data. Some ESRs got insight into complex morphologies of their study insect groups and prepared them for integration in the phylogeny. WP2, Statistical phylogenetic analysis, brought statistical phylogenetics into the efficient study of big insect groups. Statistical phylogenetics underlies almost every project in BIG4, and WP2 developed a much needed training package in RevBayes software. Several ESRs ran their phylogenetic analyses for various insect groups, some already published as peer reviewed papers. A few ESRs worked on a large collaborative dated phylogenetic analysis of the entire insect Order Coleoptera. WP3 Genomics exposed ESRs to the possibilities of genomics and next-generation sequencing techniques in biosystematics projects. ERA7 developed a cloud-based data sharing infrastructure. Some ESRs implemented Next Generation Sequencing and got phylogenetically informative markers across various target taxa, either traditionally preserved museum-based specimens or properly preserved modern DNA-tissues. WP4, Citizen-science and informatics for biodiversity, created ‘DINA-Specify’ and ‘The Naturalist’ online training packages. The SME-based ESR implemented machine learning for automated high precision identification of several insect groups. An app for citizen scientists to track distributions and abundance of Swedish ladybugs was developed and successfully implemented receiving high media attention in Sweden. WP5, Semantic publishing, outreach and dissemination, led by PENSOFT modernized the workflow for publishing huge biodiversity data about four biggest insect groups. The core development of semantic publishing is an Open Biodiversity Knowledge Management System that is already changing data publishing in the field.
All BIG4 activities are at the crossroads of several Workpackages: WP1, Big data sets assembly and compatibility for biosystematics, begun data collection. WP1 trained ESRs in extraction of huge DNA data from the suboptimal museum insect specimens, with first samples of Lepidoptera. Some ESRs produced big genomic or morphological data for a taxon-based and bulk sample-based project, which meant learning programming and de novo genome assembly for large-scale phylogenetic data. Some ESRs got insight into complex morphologies of their study insect groups and prepared them for integration in the phylogeny. WP2, Statistical phylogenetic analysis, brought statistical phylogenetics into the efficient study of big insect groups. Statistical phylogenetics underlies almost every project in BIG4, and WP2 developed a much needed training package in RevBayes software. Several ESRs ran their phylogenetic analyses for various insect groups, some already published as peer reviewed papers. A few ESRs worked on a large collaborative dated phylogenetic analysis of the entire insect Order Coleoptera. WP3 Genomics exposed ESRs to the possibilities of genomics and next-generation sequencing techniques in biosystematics projects. ERA7 developed a cloud-based data sharing infrastructure. Some ESRs implemented Next Generation Sequencing and got phylogenetically informative markers across various target taxa, either traditionally preserved museum-based specimens or properly preserved modern DNA-tissues. WP4, Citizen-science and informatics for biodiversity, created ‘DINA-Specify’ and ‘The Naturalist’ online training packages. The SME-based ESR implemented machine learning for automated high precision identification of several insect groups. An app for citizen scientists to track distributions and abundance of Swedish ladybugs was developed and successfully implemented receiving high media attention in Sweden. WP5, Semantic publishing, outreach and dissemination, led by PENSOFT modernized the workflow for publishing huge biodiversity data about four biggest insect groups. The core development of semantic publishing is an Open Biodiversity Knowledge Management System that is already changing data publishing in the field.
Research methods used in BIG4 go beyond the state-of-the-art, covering a wide methodological spectrum of modern, innovative approaches in biosystematics. The biggest breakthroughs are sequencing museum specimens for efficient phylogenetic work, implementing whole-genome approach to the phylogeny of such non-model insect group as the biggest family of rove beetles, successful implementation of the automated machine-learning based insect identification to a level of precision exceeding human performance. WP1 and WP2 interacted with WP3 Genomics, especially on aspects like DNA extraction from the suboptimally preserved museum insect specimens, bringing an amazing legacy of museum collections in the area of fast developing insect phylogenomics. This increased the scientific and societal value of the entomological collections converting them into real archives of life on Earth. WP4 and WP5 went beyond traditional biosystematics acting as a link between biosystematics and other fields of science and society. BIG4 extended and modified recent methods for morphology capture from fossil specimens through extensive use of mCT scanners. We expect potential commercial applications of BIG4 genomics activities. BIG4 also developed protocols for scanning electron microscopy (SEM), confocal laser scanning microscopy (CLSM), and micro-computed tomography (μCT) relevant to study rare specimens, rock and amber fossils. These technologies make time consuming and expensive research tools much more accessible. Much of our biodiversity knowledge is based on citizen-science efforts but biosystematics of the “big four” rarely benefit from it for lack of accessible information. BIG4 is starting to change that via the easy-to-use insect identification app developed, making citizen scientists better equipped to capture high quality data.